Need help after fixing a ground issue and cleaning the plugs finally got my bike to start and will run for about a minute before it fouls the plugs again with fuel and dies then won't start again until i pull the plugs and clean them again. I believe this is due to the airbox is currently off the bike from trying to troubleshoot. Need to know if this is the likely cause of the fuel fouling or if something else might be the issue.

the bike is a 2000 929 it has the H-VIX servo still wired in but the cables and valve are removed and it has a full exhaust installed. Other than this it is stock. It had a power commander installed but it was removed when I was troubleshooting the wiring issues. I plan on reinstalling it once a get a good map for it. Also the airbox has had the internal flapper removed when the H-VIX valve was removedand velocity stacksremoved will this drammatically affect the function. Trying to figure out how this will affect the air fuel mixture.